[gmx-users] Periodic Boundary condition

Yawar Qadri yawar at uab.edu
Mon Feb 4 18:06:42 CET 2008

I'm new at this, but I think it would be possible to add another layer of
gold above your original surface? That might be the simplest way to avoid
interactions with the opposite side of the layer. You'd also get double the
data per run.



From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Rohit
Sent: Monday, February 04, 2008 6:18 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Periodic Boundary condition


Hi Mark,
Please accept my apology for not putting a descriptive subject line.
My query is regarding the periodic boundary condition only. I read from
email archives regarding implementing periodic boundary conditions in XY
plane and not in Z direction and one can do that by increasing the size of
box in z direction by 2-3 times and thus creating a vacuum boundary.
However, in my case molecules are still moving to other side (i.e -Z) and
interacting with the gold surface. But what I want is interaction only at
the top surface not the opposite surface. 

I guess now problem is lucid.
Please help me if anything can be done to have a system where molecules can
interact only at the top surface of gold layer not the below surface.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080204/ca4b9aad/attachment.html>

More information about the gromacs.org_gmx-users mailing list